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Pylrs C-terminus domain mutant in complex with 3-benzothienyl-D- alanine and ampnp

Analyse Pylrs C-terminus domain mutant in complex with 3-benzothienyl-D- alanine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LYB
Type: protein
Length: 260 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrrolysine--tRNA ligase
EC: 6.1.1.26
UniProt: A0A0F8JXW8
Ligands: ANP, EXR, MG
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolysine--tRNA ligase (EC 6.1.1.26)	protein	260	40% helix, 24% strand	A0A0F8JXW8

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
EXR · (2R)-2-azanyl-3-(1-benzothiophen-3-yl)propanoic acid · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	476	0.69	0.79	46	ANP, EXR
2	146	0.43	0.75	27	empty
3	58	0.27	0.73	13	empty

Compared structures

6LYB · PylRS C-terminus domain mutant in complex with 3-Benzothienyl-D-alanine and AMPNP · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0F8JXW8
Elsewhere: RCSB PDB 6LYB · PDBe 6LYB · UniProt A0A0F8JXW8

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